BuddyPress RC2 will consolidate your activity streams and merge the tables. It will also go through and add any additional settings that are missing and set them as default if for some reason they do not already exist.

As long as you have not hacked the core of your install, upgrading from RC1 to RC2 should not harm any of your existing data.

There is a built in maintenance mode when using the automatic update feature of WordPress, but for something manual (such as RC1 to RC2), I might recommend something like…

The upgrade process will remove a few BuddyPress tables that are not needed anymore in RC2. Don’t worry, though. All the important data is safe. So, as long as you have a recent backup of your DB, you’ll be fine.

As far as shutting down your site during the upgrade, I usually make a post the day before stating that I’ll be performing upgrades. Since it is should take no more than 10 minutes, usually it is not an issue.

But part of the upgrade process has been to delete everything except your wp-config file, various files in /wp-content/ (and of course your database), if someone attempts to go to the site during the upgrade, there may be no files to serve. So, with more established sites, I’ll stick an index.html file in root so that it will be served if someone comes while I’m upgrading. In that file, I have the logo and a “be back soon” or something like that message. This is overkill for most sites though.

Finally, you could look at the Lock Outplugin. I’ve never used it and I do not know if it works with WPMU 2.7+.